Re: [PyMOL] Access to pymol commands from the terminal

Thank you very much! Kind regards, James 2014-09-22 18:50 GMT+02:00 Sampson, Jared : > Hi James - > > On Sep 22, 2014, at 4:30 AM, James Starlight > wrote: > > Hi Jared, > > > many thanks for the suggestion! > your method works perfect (i only slightly modified dir for input file) > > #

Re: [PyMOL] Access to pymol commands from the terminal

Hi James - On Sep 22, 2014, at 4:30 AM, James Starlight mailto:jmsstarli...@gmail.com>> wrote: Hi Jared, many thanks for the suggestion! your method works perfect (i only slightly modified dir for input file) # dock each model to the ligand for pdb in $receptors/*.pdb; do filename=$(basenam

Re: [PyMOL] Access to pymol commands from the terminal

Hi Jared, many thanks for the suggestion! your method works perfect (i only slightly modified dir for input file) # dock each model to the ligand for pdb in $receptors/*.pdb; do filename=$(basename "$pdb") M=${filename/.pdb/} echo "Processing of ${M} is initiated..." #remove water and io

Re: [PyMOL] Access to pymol commands from the terminal

Hi James - I don’t have any experience with Profit. However, instead of using "something like” PyMOL’s `super` command as you asked, you could actually use `super` in your shell session by launching PyMOL in command line mode. Of course

Re: [PyMOL] Access to pymol commands from the terminal

same sequence length. Is it >>>> possible to superimpose each structure based on some common criterium found >>>> for each mobile and reference automatically? >>>> >>>> Kind regards, >>>> >>>> James >>>> >&g

Re: [PyMOL] Access to pymol commands from the terminal

;>> >>> 2014-09-08 20:32 GMT+04:00 Markus Heller : >>> >>>> Shot in the dark, based on reading “ensemble of the structures” and >>>> “ProFit”: >>>> >>>> >>>> >>>> http://www.ncbi.nlm.nih.gov/pmc/articl

Re: [PyMOL] Access to pymol commands from the terminal

Hope that helps! Markus From: James Starlight [mailto:jmsstarli...@gmail.com<mailto:jmsstarli...@gmail.com>] Sent: Monday, September 08, 2014 6:52 AM To: pymol-users Subject: Re: [PyMOL] Access to pymol commands from the terminal Ok, ProFit has been passed :D Now I'm looking for s

Re: [PyMOL] Access to pymol commands from the terminal

>> >> >> Hope that helps! >> >> >> >> Markus >> >> >> >> *From:* James Starlight [mailto:jmsstarli...@gmail.com] >> *Sent:* Monday, September 08, 2014 6:52 AM >> *To:* pymol-users >> *Subject:* Re: [PyMOL] Access t

Re: [PyMOL] Access to pymol commands from the terminal

re ensemble > > > > Hope that helps! > > > > Markus > > > > *From:* James Starlight [mailto:jmsstarli...@gmail.com] > *Sent:* Monday, September 08, 2014 6:52 AM > *To:* pymol-users > *Subject:* Re: [PyMOL] Access to pymol commands from the terminal > &g

Re: [PyMOL] Access to pymol commands from the terminal

Ok, ProFit has been passed :D Now I'm looking for some software which could do the same least-square fitting for the ensemble of the structures taken it as the separate pdbs from the work dir (I'm not sure if the mustang software could be useful for this task)=> because looping using ProFit might

Re: [PyMOL] Access to pymol commands from the terminal

Thomas,thanks for help- I'll try to test your script! Jed, many thanks too! if I understood correctly align.profit should contain thefollowing lines: # using ProFIT to align the model to 2hi4 open $PROFIT, "> align.profit" or die "Cannot open file align.profit\n"; print $PROFIT "ATOMS CA

Re: [PyMOL] Access to pymol commands from the terminal

Hi James, adding my 2 cents to this conversation. Save the bash script below as "pymolsuper.sh". - pymolsuper.sh - #!/bin/bash if [[ $# < 2 ]]; then echo "usage: $0 mobile.pdb target.pdb [out.pdb]" exit 1 fi script="python names = cmd.get_object_list() c

Re: [PyMOL] Access to pymol commands from the terminal

Hi Jed! thanks for the advise! As I understood some commands like FIT and WRITE should be provided being INSIDE of the profit to obtain pdb output. Does it possible to do it in one line style from bash like profit ref tar output etc ? BTW profit send errors when I try to fit mob to ref and w

Re: [PyMOL] Access to pymol commands from the terminal

BTW using python script given by Matthew i've obtained error >>> execfile ('pymol.py') Traceback (most recent call last): File "", line 1, in File "pymol.py", line 2, in import pymol File "pymol.py", line 4, in pymol.finish_launching() AttributeError: 'module' object has no attrib

Re: [PyMOL] Access to pymol commands from the terminal

Thanks Tsjerk! Today I've tried some software of pairs alignment (like ce, tmalign and mammoth) and found that it's not good for me because the positions of reference and target are both altered as the result of the alignment by means of the rotational matrix superimposition method. In my case I n

Re: [PyMOL] Access to pymol commands from the terminal

Hi James, I have a light version for fitting gromacs' gro files. No time to adapt that now for PDB, but it's not too hard. ./qfit.py source.gro target.gro > output.gro Hope it helps, Tsjerk On Fri, Sep 5, 2014 at 12:31 PM, James Starlight wrote: > should to add > > than I've used both TMali

Re: [PyMOL] Access to pymol commands from the terminal

should to add than I've used both TMalign and mammoth utilities but didn't understand how to obtain superimposed output as the full-atomic pdb's. I will be thankful if someone could share with me its experience :) James 2014-09-05 12:00 GMT+02:00 James Starlight : > Thanks Matthew, > > > I'll

Re: [PyMOL] Access to pymol commands from the terminal

Thanks Matthew, I'll try to use this opportunity! BTW does anybody knows some simple Linux utility to perform structural superimposition of 2 pdbs and obtain the superimposed (target.pdb) in separate pdb file? This time I'm writing big docking script where I need to superimpose each receptor agai

Re: [PyMOL] Access to pymol commands from the terminal

You could make a python script that import pymol and does what you want from there. Some thing like this (untested); import __main__ __main__.pymol_argv = ['pymol','-cqk'] # Pymol: quiet and no GUI import pymol pymol.finish_launching() from pymol import cmd reffile = sys.argv[1] tarfile = s

Re: [PyMOL] Access to pymol commands from the terminal

thanks! and do I need to pipe the below command to smth grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb > merged.pdb if I need to change 'END' to 'TER' in the merged.pdb ? 2014-09-04 16:54 GMT+02:00 James Starlight : > thanks! > > and do I need to pipe the below command to smth > gr

Re: [PyMOL] Access to pymol commands from the terminal

Use the -h flag with grep to suppress the filename. Also, you don't need to pipe to cat, you can write directly to the file. grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb > merged.pdb On 09/04/2014 10:38 AM, James Starlight wrote: ..and one question about grep (really didn't find

Re: [PyMOL] Access to pymol commands from the terminal

..and one question about grep (really didn't find it in the tutorial) using grep '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb |cat > merged.pdb I've obtained good pdb BUT each line prior to the ATOM the name of the pdb of the previous files have been added eg: tarr_se.pdb:ATOM 1 N A

Re: [PyMOL] Access to pymol commands from the terminal

one question :) could someone explain me the ussage the pymol commands from the shell on the example e.g i need to load 2 pdbs in pymol make its superimposition and than save one of the superimposed pdb like load ref.pdb tar.pdb super tar, ref save tar > tar_superimposed.pdb I've tried to do part

Re: [PyMOL] Access to pymol commands from the terminal

(sed '1d' protein.pdb; sed '1d' lipid.pdb) > merged.pdb --or-- tail -q -n '+2' protein.pdb lipid.pdb > merged.pdb -David On Thu, Sep 4, 2014 at 6:19 AM, James Starlight wrote: > Hi Tsjerk, > > Thanks alot! > Also I have the task to merge protein.pdb and lipids.pdb with some 1 line > shell

Re: [PyMOL] Access to pymol commands from the terminal

Hi James, grep '^\(ATOM\|HETATM\|CRYST1\)' protein.pdb lipid.pdb > merged.pdb Oh, the joy one has from reading a sed/grep/awk tutorial :) Cheers, Tsjerk On Thu, Sep 4, 2014 at 12:19 PM, James Starlight wrote: > Hi Tsjerk, > > Thanks alot! > Also I have the task to merge protein.pdb and lip

Re: [PyMOL] Access to pymol commands from the terminal

Hi Tsjerk, Thanks alot! Also I have the task to merge protein.pdb and lipids.pdb with some 1 line shell command ( like CAT) to obtain protein inserted in the lipids (the seccond file is consist of the whole which can locate the protein). My problem is that both protein.pdb and lipids.pdb consisted

Re: [PyMOL] Access to pymol commands from the terminal

Hi James, You can use pymol -cd "pymolcommands". See http://www.pymolwiki.org/index.php/Command_Line_Options However, the first part is much easier with grep or sed. To remove all solvent molecules: grep -v "^ATOM.*SOL" in.pdb > out.pdb To remove NA+/CL- too grep -v "ATOM.*\(SOL\|NA+\|CL-\)" i

[PyMOL] Access to pymol commands from the terminal

Dear PyMol users! I'd like to find possibilities for running of some pymol commands from the terminal. For instance in my case I' d like perform 2 simple steps (both in terminal not in the pymol GUI) to remove water and ions from my target input pdb (typical I do it via gromacs editconf) superimpo